8S6E | pdb_00008s6e

Monoclonal antibody MenW targeting serogroup W of Neisseria meningitidis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 
    0.223 (Depositor), 0.190 (DCC) 
  • R-Value Work: 
    0.201 (Depositor) 
  • R-Value Observed: 
    0.201 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history

Literature

Antigenic determinants driving serogroup-specific antibody response to Neisseria meningitidis C, W, and Y capsular polysaccharides: Insights for rational vaccine design.

Pietri, G.P.Bertuzzi, S.Karnicar, K.Unione, L.Lisnic, B.Malic, S.Miklic, K.Novak, M.Calloni, I.Santini, L.Usenik, A.Romano, M.R.Adamo, R.Jonjic, S.Turk, D.Jimenez-Barbero, J.Lenac Rovis, T.

(2024) Carbohydr Polym 341: 122349-122349

  • DOI: https://doi.org/10.1016/j.carbpol.2024.122349
  • Primary Citation Related Structures: 
    8S6E

  • PubMed Abstract: 

    Meningococcal glycoconjugate vaccines sourced from capsular polysaccharides (CPSs) of pathogenic Neisseria meningitidis strains are well-established measures to prevent meningococcal disease. However, the exact structural factors responsible for antibody recognition are not known. CPSs of Neisseria meningitidis serogroups Y and W differ by a single stereochemical center, yet they evoke specific immune responses. Herein, we developed specific monoclonal antibodies (mAbs) targeting serogroups C, Y, and W and evaluated their ability to kill bacteria. We then used these mAbs to dissect structural elements responsible for carbohydrate-protein interactions. First, Men oligosaccharides were screened against the mAbs using ELISA to select putative lengths representing the minimal antigenic determinant. Next, molecular interaction features between the mAbs and serogroup-specific sugar fragments were elucidated using STD-NMR. Moreover, X-ray diffraction data with the anti-MenW CPS mAb enabled the elucidation of the sugar-antibody binding mode. Our findings revealed common traits in the epitopes of all three sialylated serogroups. The minimal binding epitopes typically comprise five to six repeating units. Moreover, the O-acetylation of the neuraminic acid moieties was fundamental for mAb binding. These insights hold promise for the rational design of optimized meningococcal oligosaccharides, opening new avenues for novel production methods, including chemical or enzymatic approaches.


  • Organizational Affiliation
    • Center for Proteomics, Faculty of Medicine, University of Rijeka, Rijeka, Croatia.

Macromolecule Content 

  • Total Structure Weight: 48.02 kDa 
  • Atom Count: 3,623 
  • Modeled Residue Count: 438 
  • Deposited Residue Count: 438 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
MenW.01 Heavy chain224Mus musculusMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
MenW.01 Light chain214Mus musculusMutation(s): 0 

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NA

Query on NA



Download:Ideal Coordinates CCD File
C [auth B]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free:  0.223 (Depositor), 0.190 (DCC) 
  • R-Value Work:  0.201 (Depositor) 
  • R-Value Observed: 0.201 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.87α = 90
b = 69.16β = 90
c = 128.98γ = 90
Software Package:
Software NamePurpose
MAINrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing
MAINmodel building

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
H2020 Marie Curie Actions of the European CommissionEuropean Union675671
European Regional Development FundEuropean UnionKK.01.1.1.01.0006
Ministry of Science, Education and Sports of the Republic of CroatiaCroatiaKK.01.1.1.01.0006
Slovenian Research AgencySloveniaP1-0048
Slovenian Research AgencySloveniaIO-0048

Revision History  (Full details and data files)

  • Version 1.0: 2024-06-26
    Type: Initial release
  • Version 1.1: 2024-10-16
    Changes: Structure summary